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We will start with a set of short sequence reads and associated base quality scores (stored in a fastq file), find the most likely genomic location for each read (producing a BAM file), generate an initial list of polymorphic sites and genotypes (stored in a VCF file) and use haplotype information to refine these genotypes (resulting in an updated VCF file).
We will start with a set of short sequence reads and associated base quality scores (stored in a fastq file), find the most likely genomic location for each read (producing a BAM file), generate an initial list of polymorphic sites and genotypes (stored in a VCF file) and use haplotype information to refine these genotypes (resulting in an updated VCF file).
=== Polymutt ===
=== Note ===
If you are interested in ''de novo'' mutations or are working on families with deep sequence data, you should also consider our sister program, [http://genome.sph.umich.edu/wiki/Polymutt Polymutt], which ignores linkage disequilibrium information but can handle more complex pedigrees.
If you are interested in ''de novo'' mutations or are working on one or two families with deep sequence data (>30X), you should first consider our sister program, [http://genome.sph.umich.edu/wiki/Polymutt Polymutt], which ignores linkage disequilibrium information but can handle more complex pedigrees.
=== Download ===
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